Pharmaceutical Research in the Cloud

Jason Stowe (Cycle Computing)
Cloud Computing
Location: Portland 251
Tags: cloud, chef, ec2, aws, vpc, condor
Average rating: *****
(5.00, 4 ratings)

Life science research, including molecular modeling, bioinformatics, proteomics and genomics are ripe with examples of open-source technology. In this presentation, Stowe will present the use of open software in managing state-of-the-art high performance computing (HPC) environments and provisioning auto-configuring software stacks in internal clouds and Amazon EC2.

Research Workflows
Many pharmaceutical and other organizations use pure open-source technology like the Condor Project ( and mixed open-source like Sun GridEngine ( to manage HPC clusters. The calculations frequently utilize open tools in their software stack, including Gromacs, Blast, and R. Stowe will illustrate the software pipelines commonly used in pharmaceutical research and methods for deploying these software stacks in clouds.

HPC and “Cloudbursting”
We will discuss using Condor to make the most of internal resources by harvesting compute cycles on dedicated servers, idle workstations and under-utilized virtual environments. Covered architectures will also include features for power management and the ability for researchers to “cloudburst” when internal capacity is exceeded, with specific considerations for synchronizing the data involved for these calculations.

Photo of Jason Stowe

Jason Stowe

Cycle Computing

Jason Stowe is the CEO of Cycle Computing (, a provider of high performance computing and open source technology in the cloud. Cycle helps to provision large-scale, secure HPC clusters in the cloud on demand. Using open schedulers like Condor ( and SGE to provide grid functionality and reduce costs, Cycle manages small clusters to grids of more than 30,000 CPUs. Starting with three Fortune 100 clients in financial services, Cycle now deploys production grids at Fortune 500s, government research and academic institutions. A seasoned entrepreneur and experienced technologist; Stowe attended Carnegie Mellon and Cornell and is on Amazon Web Services’ Customer Advisory Board.

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Cory Engebretson
07/21/2010 1:46pm PDT

Good info, and the presentation format was engaging.

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